vispr server rendering bug, QC data

[Former user]

VISPR server used to render QC data very quickly and now takes a VERY long time to render QC data. The bug seems to be proportional to the number of sgRNAs in the library, rather than the number of samples or reads. My conda environment is as follows below. VISPR is no longer useable/useful with this bug that seems to have been introduced by an updated dependency.

(mageck-vispr) poirij03-mba13:mageck2 poirij03$ conda list

packages in environment at /Users/poirij03/miniconda3/envs/mageck-vispr:

Name Version Build Channel

_r-mutex 1.0.0 anacondar_1
aioeasywebdav 2.4.0 py36_1000 conda-forge aiohttp 3.6.2 py36h1de35cc_0
appdirs 1.4.3 py36h28b3542_0
appnope 0.1.0 py36hf537a9a_0
asn1crypto 1.2.0 py36_0
async-timeout 3.0.1 py_1000 conda-forge attrs 19.3.0 py_0
backcall 0.1.0 py36_0
bcrypt 3.1.7 py36h1de35cc_0
bioconductor-annotate 1.64.0 r36_0 bioconda bioconductor-annotationdbi 1.48.0 r36_0 bioconda bioconductor-biobase 2.46.0 r36h01d97ff_0 bioconda bioconductor-biocgenerics 0.32.0 r36_0 bioconda bioconductor-genefilter 1.68.0 r36ha90c164_0 bioconda bioconductor-iranges 2.20.0 r36h01d97ff_0 bioconda bioconductor-s4vectors 0.24.0 r36h01d97ff_0 bioconda bioconductor-sva 3.15.0 0 bioconda blas 1.0 mkl
boto3 1.10.39 py_0
botocore 1.13.39 py_0
bwidget 1.9.11 1
bz2file 0.98 py36_1
bzip2 1.0.8 h1de35cc_0
ca-certificates 2019.11.27 0
cachetools 2.1.0 py_0 conda-forge cairo 1.16.0 h0ab9d94_1001 conda-forge cctools 895 1
certifi 2019.11.28 py36_0
cffi 1.13.2 py36hb5b8e2f_0
chardet 3.0.4 py36_1003
clang 4.0.1 1
clang_osx-64 4.0.1 h1ce6c1d_18
clangxx 4.0.1 1
clangxx_osx-64 4.0.1 h22b1bf0_18
click 7.0 py36_0
compiler-rt 4.0.1 hcfea43d_1
configargparse 0.14.0 py36_0
cryptography 2.8 py36ha12b0ac_0
curl 7.67.0 ha441bb4_0
cutadapt 2.5 py36h01d97ff_0 bioconda datrie 0.8 py36h1de35cc_0
decorator 4.4.1 py_0
dnaio 0.3 py36h1de35cc_1 bioconda docutils 0.15.2 py36_0
dropbox 9.4.0 py36_0
expat 2.2.6 h0a44026_0
fastqc 0.11.8 2 bioconda fftw 3.3.8 nompi_h5c49c53_1106 conda-forge filechunkio 1.6 py36_0 bioconda flask 1.1.1 py_0
font-ttf-dejavu-sans-mono 2.37 h6964260_0
fontconfig 2.13.1 h1027ab8_1000 conda-forge freetype 2.9.1 hb4e5f40_0
fribidi 1.0.5 h1de35cc_0
ftputil 3.2 py36_0 bioconda gdk-pixbuf 2.36.12 h284f8de_1003 conda-forge gettext 0.19.8.1 h15daf44_3
gfortran_osx-64 4.8.5 h22b1bf0_8
ghostscript 9.18 1 bioconda giflib 5.1.7 h01d97ff_1 conda-forge gitdb2 2.0.6 py_0
gitpython 3.0.5 py_0
glib 2.63.1 hd977a24_0
gobject-introspection 1.58.2 py36h93883a9_1002 conda-forge google-api-core 1.14.3 py36_0 conda-forge google-auth 1.2.1 py_0 conda-forge google-cloud-core 1.0.3 py_0 conda-forge google-cloud-storage 1.20.0 py_0 conda-forge google-resumable-media 0.4.1 py_0 conda-forge googleapis-common-protos 1.6.0 py36_0
graphite2 1.3.13 h2098e52_0
graphviz 2.40.1 hefbbd9a_2
gsl 2.4 h1de35cc_4
harfbuzz 1.8.8 hb8d4a28_0
icu 58.2 h4b95b61_1
idna 2.8 py36_0
idna_ssl 1.1.0 py36_1000 conda-forge imagemagick 7.0.8_65 pl526he2cbc91_0 conda-forge importlib_metadata 1.3.0 py36_0
intel-openmp 2019.4 233
ipython 7.10.2 py36h39e3cac_0
ipython_genutils 0.2.0 py36_0
itsdangerous 1.1.0 py36_0
jbig 2.1 h1de35cc_2001 conda-forge jedi 0.15.1 py36_0
jinja2 2.10.3 py_0
jmespath 0.9.4 py_0 conda-forge joblib 0.14.1 py_0
jpeg 9c h1de35cc_1001 conda-forge jsonschema 3.2.0 py36_0
krb5 1.16.4 hddcf347_0
ld64 274.2 1
libcroco 0.6.13 hc484408_0 conda-forge libcurl 7.67.0 h051b688_0
libcxx 4.0.1 hcfea43d_1
libcxxabi 4.0.1 hcfea43d_1
libedit 3.1.20181209 hb402a30_0
libffi 3.2.1 1 bioconda libgcc 4.8.5 hdbeacc1_10
libgfortran 3.0.1 h93005f0_2
libiconv 1.15 hdd342a3_7
libpng 1.6.37 ha441bb4_0
libprotobuf 3.11.2 hd9629dc_0
librsvg 2.46.2 h1ccd86b_1 conda-forge libsodium 1.0.16 h3efe00b_0
libssh2 1.8.2 ha12b0ac_0
libtiff 4.1.0 hcb84e12_0
libwebp 1.0.2 h20df551_3 conda-forge libxcb 1.13 h1de35cc_1002 conda-forge libxml2 2.9.9 hf6e021a_1
llvm 4.0.1 1
llvm-lto-tapi 4.0.1 1
llvm-openmp 4.0.1 hcfea43d_1
mageck 0.5.9.2 py36h770b8ee_0 bioconda mageck-vispr 0.5.4 py_2 bioconda make 4.2.1 h3efe00b_1
markupsafe 1.1.1 py36h1de35cc_0
mkl 2019.4 233
mkl-service 2.3.0 py36hfbe908c_0
mkl_fft 1.0.15 py36h5e564d8_0
mkl_random 1.1.0 py36ha771720_0
more-itertools 8.0.2 py_0
multidict 4.5.2 py36h1de35cc_1000 conda-forge ncurses 6.1 h0a44026_1
networkx 2.4 py_0
numpy 1.17.4 py36h890c691_0
numpy-base 1.17.4 py36h6575580_0
openjdk 8.0.152 h393ad39_1
openjpeg 2.3.1 hdc36067_1 conda-forge openssl 1.1.1d h1de35cc_3
pandas 0.25.3 py36h0a44026_0
pango 1.42.4 h060686c_0
paramiko 2.6.0 py36_0
parso 0.5.2 py_0
pcre 8.43 h0a44026_0
perl 5.26.2 h4e221da_0
pexpect 4.7.0 py36_0
pickleshare 0.7.5 py36_0
pigz 2.4 ha441bb4_0
pip 19.3.1 py36_0
pixman 0.38.0 h1de35cc_0
pkg-config 0.29.2 h112b980_1005 conda-forge prettytable 0.7.2 py_3 conda-forge prompt_toolkit 3.0.2 py_0
protobuf 3.11.2 py36h0a44026_0
psutil 5.6.7 py36h1de35cc_0
pthread-stubs 0.4 h1de35cc_1001 conda-forge ptyprocess 0.6.0 py36_0
pyasn1 0.4.8 py_0
pyasn1-modules 0.0.5 py36_0 bioconda pycparser 2.19 py36_0
pygments 2.5.2 py_0
pygraphviz 1.3.1 py36_0 bioconda pynacl 1.3.0 py36h1de35cc_0
pyopenssl 19.1.0 py36_0
pyrsistent 0.15.6 py36h1de35cc_0
pysftp 0.2.9 py36_0 bioconda pysocks 1.7.1 py36_0
python 3.6.9 h359304d_0
python-dateutil 2.8.0 py36_0
python-irodsclient 0.7.0 py_0 conda-forge pytz 2019.3 py_0
pyyaml 5.2 py36h1de35cc_0
r 3.6.0 r36_0
r-assertthat 0.2.1 r36h6115d3f_0
r-base 3.6.1 hcb44179_1
r-bh 1.69.0_1 r36h6115d3f_0
r-bit 1.1_14 r36h46e59ec_0
r-bit64 0.9_7 r36h46e59ec_0
r-bitops 1.0_6 r36h46e59ec_4
r-blob 1.1.1 r36h6115d3f_0
r-boot 1.3_20 r36h6115d3f_0
r-class 7.3_15 r36h46e59ec_0
r-cli 1.1.0 r36h6115d3f_0
r-cluster 2.0.8 r36hfffe0aa_0
r-codetools 0.2_16 r36h6115d3f_0
r-crayon 1.3.4 r36h6115d3f_0
r-dbi 1.0.0 r36h6115d3f_0
r-dbplyr 1.4.0 r36h6115d3f_0
r-digest 0.6.18 r36h46e59ec_0
r-dplyr 0.8.0.1 r36h466af19_0
r-fansi 0.4.0 r36h46e59ec_0
r-foreign 0.8_71 r36h46e59ec_0
r-gdata 2.18.0 r36h6115d3f_0 r r-glue 1.3.1 r36h46e59ec_0
r-gtools 3.8.1 r36h46e59ec_0 r r-kernsmooth 2.23_15 r36hfffe0aa_4
r-lattice 0.20_38 r36h46e59ec_0
r-magrittr 1.5 r36h6115d3f_4
r-mass 7.3_51.3 r36h46e59ec_0
r-matrix 1.2_17 r36h46e59ec_0
r-memoise 1.1.0 r36h6115d3f_0
r-mgcv 1.8_28 r36h46e59ec_0
r-nlme 3.1_139 r36hfffe0aa_0
r-nnet 7.3_12 r36h46e59ec_0
r-pillar 1.3.1 r36h6115d3f_0
r-pkgconfig 2.0.2 r36h6115d3f_0
r-plogr 0.2.0 r36h6115d3f_0
r-prettyunits 1.0.2 r36h6115d3f_0
r-purrr 0.3.2 r36h46e59ec_0
r-r6 2.4.0 r36h6115d3f_0
r-rcpp 1.0.1 r36h466af19_0
r-rcurl 1.95_4.12 r36h46e59ec_0
r-recommended 3.6.0 r36_0
r-rlang 0.3.4 r36h46e59ec_0
r-rpart 4.1_15 r36h46e59ec_0
r-rsqlite 2.1.1 r36h466af19_0
r-spatial 7.3_11 r36h46e59ec_4
r-survival 2.44_1.1 r36h46e59ec_0
r-tibble 2.1.1 r36h46e59ec_0
r-tidyselect 0.2.5 r36h466af19_0
r-utf8 1.1.4 r36h46e59ec_0
r-xml 3.98_1.19 r36h46e59ec_0
r-xtable 1.8_4 r36h6115d3f_0
ratelimiter 1.2.0 py36_1000 conda-forge readline 7.0 h1de35cc_5
requests 2.22.0 py36_1
rpy2 2.9.4 py36r36h1d22016_0
rsa 3.1.4 py36_0 bioconda s3transfer 0.2.1 py36_0
scikit-learn 0.22 py36h27c97d8_0
scipy 1.3.2 py36h1410ff5_0
setuptools 42.0.2 py36_0
six 1.13.0 py36_0
smmap2 2.0.5 py36_0
snakemake 5.9.1 0 bioconda snakemake-minimal 5.9.1 py_0 bioconda sqlite 3.30.1 ha441bb4_0
tk 8.6.8 ha441bb4_0
tktable 2.10 h1de35cc_0
traitlets 4.3.3 py36_0
typing_extensions 3.7.4.1 py36_0
urllib3 1.25.7 py36_0
vispr 0.4.15 py_0 bioconda wcwidth 0.1.7 py36_0
werkzeug 0.16.0 py_0
wheel 0.33.6 py36_0
wrapt 1.11.2 py36h1de35cc_0
xmlrunner 1.7.7 py_0 conda-forge xopen 0.7.3 py_0 bioconda xorg-kbproto 1.0.7 h1de35cc_1002 conda-forge xorg-libice 1.0.10 h01d97ff_0 conda-forge xorg-libsm 1.2.3 h01d97ff_1000 conda-forge xorg-libx11 1.6.9 h0b31af3_0 conda-forge xorg-libxau 1.0.9 h1de35cc_0 conda-forge xorg-libxdmcp 1.1.3 h01d97ff_0 conda-forge xorg-libxext 1.3.4 h01d97ff_0 conda-forge xorg-libxrender 0.9.10 h01d97ff_1002 conda-forge xorg-libxt 1.2.0 h01d97ff_0 conda-forge xorg-renderproto 0.11.1 h1de35cc_1002 conda-forge xorg-xextproto 7.3.0 h1de35cc_1002 conda-forge xorg-xproto 7.0.31 h1de35cc_1007 conda-forge xz 5.2.4 h1de35cc_4
yaml 0.1.7 hc338f04_2
yarl 1.4.2 py36h1de35cc_0
zipp 0.6.0 py_0
zlib 1.2.11 h1de35cc_3
zstd 1.3.7 h5bba6e5_0